Life Sciences - Literature References
LIFE SCIENCE (GENERAL)
Visual exploration of HTS databases: bridging the gap between chemistry and biology
Christopher Ahlberg
Drug Discovery Today, Aug 1999 4(8):370-76
Intuitive data analysis: The next generation
Bill Ladd
Modern Drug Discovery, 2000 3(1):46-52
information visualization and analytical data mining in R&D
Bill Ladd, Shawn Kenner
Current Opinion in Drug Discovery & Development 2000 3(3):280-291
Collaborative Data Analysis Accelerates Drug Discovery Process
Paul A. Clemons
Scientific Computing & Instrumentation, Apr 2003, 20(5):36-42, www.scimag.com
Software Tools Navigate the Rising Data Tide
Sean Keating
Drug Discovery & Development, Oct 2002, www.dddmag.com
The race to computerise biology
The Economist, Dec 2002, www.economist.com
Integrated data- and decision analytics workflow in modern drug discovery and development
Mark Demesmaeker
Chemistry Today, Oct/Nov 2001, 19(11/11):17-21
analytic applications: Fighting the Clock with Analytics
Matt Anstett
Drug Delivery Technology, May 2004, 4(4) http://drugdeliverytech.com/cgi-bin/current_issue.cgi
High-Throughput analytics tackle the bottleneck in data handling
Bill Ladd
Modern Drug Discovery, May 2004, 43-47, http://pubs.acs.org/subscribe/journals/mdd/v07/i05/html/504ladd.html
LIFE SCIENCE (HTS)
Leveraging process integration in early drug discovery
Nicolas Fay and Dirk Ullmann
Drug Discovery Technology, 2002, 7(20) (Suppl.)
Screening informatics: adding value with meta-data, structures and visualization tools
Bryn R. Roberts
Drug Discovery Today: HTS Supplement, Jun 2000 1(1):10-14
Creating Knowledge From HTS Data
Julia Boguslavsky
Drug Discovery & Development, Jun 2001, www.dddmag.com
High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate
Michela Zolli-Juran, Jonathan D. Cechetto, Rebecca Hartlen, Denis M. Daigle and Eric D. Brown, Bioorganic & Medicinal Chemistry Letters, 13 (15) , 4 August 2003, 2493-2496
Fluorescence readouts in HTS: No gain without pain?
Philip Gribbon and Andreas Sewing
Drug Discovery Today, 8(22) 2003, 1035-43, www.drugdiscoverytoday.com
High content screening applied to large-scale biology
Vivek C. Abraham, D. Lansing Taylor and Jeffrey R. Haskins
TRENDS in Biotechnology, 2004, 22 (1), 15-22.
LIFE SCIENCE (FUNCTIONAL GENOMICS)
Informatics and multivariate analysis of toxicogenomics data
Salter AH, Nilsson KC.
Current Opinion in Drug Discovery & Development 2003 6(1):117-122
Prediction of clinical drug efficacy by classification of drug-induced genomic expression profiles in vitro
Erik C. Gunther, David J. Stone, Robert W. Gerwien, Patricia Bento, and Melvyn P. Heyes
PNAS, Aug 2003 100(16):9608-13, http://www.pnas.org/cgi/content/full/100/16/9608
Shaping Gene Expression in Activated and Resting Primary Macrophages by IL-101
Roland Lang, Divyen Patel, John J. Morris, Robert L. Rutschman, and Peter J. Murray
Journal of Immunology, Sep 2002, 169: 2253 - 2263
Case Study: Spotfire allows Harvard Medical School and Infinity to cooperate on annotating Chemogenomic libraries
Paul A. Clemons
Biotech Tech, May 2003 2(5):22-23
Analysis of Shuffled Gene Libraries
John M. Joern, Peter Meinhold and Frances H. Arnold
J Mol Biol, 2002, 316, 643-656
Discovery and development of a genomic drug
Donna Morgan Murray & Richard Shimkets, CuraGen, USA
Current Drug Discovery, Jun 2003, 27-33, www.currentdrugdiscovery.com
(no specific mention of Spotfire, but screenshots)
Chemical Genomics Advances New Medicines
Paul E. Young, Ph.D., and David K. Bol, Ph.D.
Genetic Engineering News, Jan 2003, 1(1):1-3, www.genengnews.com
(no specific mention of Spotfire, but screenshots)
bioinformatics: Bringing order from chaos
David Robbins
BioPeople, Summer 2000, 31, pp 42-49
Making Sense of Microchip Array Data
Michael Brush
The Scientist, Apr. 30, 2001, 15(9):25
http://www.the-scientist.com/yr2001/apr/profile1_010430.html
Data Analysis Tools for DNA Microarrays
Sorin Draghici (contributing Author: Matthew J. Anstett)
CRC Mathematical Biology and Medicine Series, Chapman & Hall, 2003, ISBN: 1584883154
Visualization of regional gene expression biases by microarray data sorting
Ronald van Eijk, Jan Oosting, Nathalie Sieben, Tom van Wezel, and Anne-Marie Cleton-Jansen
Biotechniques. 2004 Apr;36(4):592-4, 596
Previously unidentified changes in renal cell carcinoma gene expression identified by parametric analysis of microarray data
Marc E Lenburg, Louis S Liou, Norman P Gerry, Garrett M Frampton,
Herbert T Cohen and Michael F Christman
BMC Cancer, 2003, 3:31
Interferon-Induced Sensitization of Colon Carcinomas to ZD9331
Targets Caspases, Downstream of Fas, Independent of Mitochondrial Signaling and the Inhibitor of Apoptosis Survivin
James Geller, Istvan Petak, Kinga Szekely Szucs, Katalin Nagy, David M. Tillman, and Janet A. Houghton
Clinical Cancer Research, 2003, Vol. 9, 6504–6515
The influence of tumor size and environment on gene expression in commonly used human tumor lines
Michael A Gieseg, Michael Z Man, Nicholas A Gorski, Steven J Madore, Eric P Kaldjian, and Wilbur R Leopold
Pfizer Global Research and Development, 2800 Plymouth Rd, Ann Arbor, Michigan, 48105, USA
BMC Cancer 2004, 4:35 doi:10.1186/1471-2407-4-35;
http://www.biomedcentral.com/1471-2407/4/35
information visualization techniques in bioinformatics during the postgenomic era
YingTao,YangLiu, Carol Friedman and Yves A. Lussier
DDT: BIOSILICO, Vol. 2. No.6 November 2004
www.drugdiscoverytoday.com
An Evaluation of Microarray Visualization Tools for Biological Insight
Purvi Saraiya, Chris North, and Karen Duca
InfoVis, 2004
GECKO: a complete large-scale gene expression analysis platform
Joachim Theilhaber, Anatoly Ulyanov, Anish Malanthara, Jack Cole, Dapeng Xu, Robert Nahf, Michael Heuer, Christoph Brockel and Steven Bushnell
BMC bioinformatics, 2004, 5:195
http://www.biomedcentral.com/1471-2105/5/195/
Expression profiling of the developing and mature Nrl2/2 mouse retina: identification of retinal disease candidates and transcriptional regulatory targets of Nrl
Shigeo Yoshida, Alan J. Mears, James S. Friedman, Todd Carter, Shirley He, Edwin Oh1, Yuezhou Jing, Rafal Farjo, Gilles Fleury, Carrolee Barlow, Alfred O. Hero and Anand Swaroop
Human Molecular Genetics, 2004, Vol. 13, No. 14 1487-1503
http://www.umich.edu/~retina/publications/Yoshida2004.pdf
LIFE SCIENCE (LEAD DISCOVERY)
Protein-Ligand Interactions: From Molecular Recognition to Drug Design
H.-J. Bohm and G. Schneider (Editors)
Methods and Principle of Medicinal Chemistry, Wiley-VCH, Weinheim, 2003 ISBN 3-527-30521-1, 213-236
Decision analytics in life science discovery through visual integration of chemical and biological information on the desktop
Mark Demesmaeker
Rational Approaches to Drug Design, H.-D. Höltje and W. Sippl, eds., Prous, Barcelona (2001) ISBN 84-8124-176-8
Much ado about data
Peter Gund, Mike Dippolito & Yvonne Shimshock, Gund Discovery Services & DeltaSoft Inc
Current Drug Discovery, Feb 2003, 29-32, www.currentdrugdiscovery.com
Chemoinformatics and Drug Discovery
Jun Xu and Arnold Hagler
Molecules 2002, 7, 566-600, http://www.mdpi.org
Generating Diverse Skeletons of Small Molecules Combinatorially
Martin D. Burke, Eric M. Berger, and Stuart L. Schreiber
Science Oct. 24, 2003, S1-46
HAD: An Automated Database Tool for Analyzing Screening Hits in Drug Discovery
Jian Shen
J. Chem. Inf. Comput. Sci. 2003, 43, 1668-1672
Metabonomics
A H NMR-based metabonomic study of urin and plasma samples obtained from healthy human subjucts
E.M. Lenz, J. Bright, I.D. Wilson, S.R. Morgan, A.F.P. Nash
Journal of Pharmaceutical and Biomedical Analysis, 2003, 33:1103-1115
Preclinical ADME
Implementation of an ADME enabling selection and visualization tool for drug discovery
Chad L. Stoner, Eric Gifford, Charles Stankovic, Christopher S. Lepsy, Joanne Brodfuehrer, J. V. N. Vara Prasad, Narayanan Surendran
Journal of Pharmaceutical Sciences, 2004, 93(5), 1131-1141.
Automated high hhroughput ADME assays for metabolic stability and cytochrome P450 inhibition profiling of combinatorial libraries
Kelly M. Jenkins, Reginald Angeles, Marianne T. Quintos, Rongda Xu,
Daniel B. Kassel, Robyn A. Rourick
Journal of Pharmaceutical and Biomedical Analysis, 2004, 34:989–1004